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BioC 3.5: CHECK report for chimeraviz on malbec2

This page was generated on 2017-10-18 14:18:15 -0400 (Wed, 18 Oct 2017).

Package 204/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chimeraviz 1.0.4
Stian Lågstad
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/chimeraviz
Branch: RELEASE_3_5
Last Commit: f885080
Last Changed Date: 2017-10-15 07:48:18 -0400 (Sun, 15 Oct 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: chimeraviz
Version: 1.0.4
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings chimeraviz_1.0.4.tar.gz
StartedAt: 2017-10-17 21:53:18 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:00:15 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 416.7 seconds
RetCode: 0
Status:  OK 
CheckDir: chimeraviz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings chimeraviz_1.0.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/chimeraviz.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chimeraviz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chimeraviz’ version ‘1.0.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘Biostrings’ ‘GenomicRanges’ ‘IRanges’ ‘Gviz’ ‘S4Vectors’ ‘ensembldb’
  ‘AnnotationFilter’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘chimeraviz’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    extdata   2.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
plotFusion                 14.944  1.620  16.809
plotTranscripts             6.780  0.620   7.406
plotFusionTranscriptsGraph  7.208  0.000   7.210
plotFusionTranscript        6.336  0.000   6.341
createFusionReport          5.020  0.256   7.931
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/chimeraviz.Rcheck/00check.log’
for details.


chimeraviz.Rcheck/00install.out:

* installing *source* package ‘chimeraviz’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (chimeraviz)

chimeraviz.Rcheck/chimeraviz-Ex.timings:

nameusersystemelapsed
addFusionReadsAlignment1.0040.0161.213
createFusionReport5.0200.2567.931
decideTranscriptCategory0.4600.0200.479
downstreamPartnerGene0.0840.0080.093
fetchReadsFromFastq000
fusionSpanningReadsCount0.0600.0000.062
fusionSplitReadsCount0.0360.0040.041
fusionToDataFrame0.0480.0000.046
getEnsemblIds0.6240.0040.644
getFusionByChromosome0.0680.0000.065
getFusionByGeneName0.0640.0000.063
getFusionById0.0680.0040.069
getTranscriptsEnsembldb4.6360.0084.649
importDefuse0.1120.0000.112
importEricscript0.1320.0000.131
importFusioncatcher0.1800.0000.179
importFusionmap0.1560.0000.157
importInfusion0.1120.0000.116
importJaffa0.1000.0040.106
importPrada0.1080.0000.110
importSoapfuse0.1120.0000.110
importStarfusion0.1240.0000.126
partnerGeneEnsemblId0.0840.0000.087
partnerGeneJunctionSequence0.0480.0000.048
plotCircle1.1400.0201.163
plotFusion14.944 1.62016.809
plotFusionReads0.7720.1000.870
plotFusionTranscript6.3360.0006.341
plotFusionTranscriptsGraph7.2080.0007.210
plotTranscripts6.7800.6207.406
selectTranscript3.3080.0043.314
splitOnUtrAndAddFeature0.2520.0000.251
upstreamPartnerGene0.0800.0000.079
writeFusionReference0.0440.0040.045